Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ProbabilityAnalyserKickstarter	14	98	26	0.00%	Show methods

Class ProbabilityAnalyserKickstarter

Class ProbabilityAnalyserKickstarter	Line # 14	Total Statements 98	Complexity 26	TOTAL Coverage 0.00%
main(String[]) : void   main(String[]) : void	1717	98.098	26.026	0.0 0.00%

 

Contributing tests

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1		package jalview.util;
2
3		import java.io.IOException;
4		import java.util.Scanner;
5
6		/**
7		* This class contains the brain of the analyser program, and contains a number
8		* of commands for the processing of data.
9		*
10		* @author TZVanaalten
11		*
12		*/
13
		0% Uncovered Elements: 131 (131) Complexity: 26 Complexity Density: 0.27
14		public class ProbabilityAnalyserKickstarter
15		{
16
		0% Uncovered Elements: 130 (130) Complexity: 26 Complexity Density: 0.27
17	0	public static void main(String[] args)...
18		throws IOException, InterruptedException
19		{
20
21		// this does all of the processing
22	0	HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
23
24	0	boolean running = true;
25	0	System.out.println("ACTIVATED");
26	0	while (running)
27		{
28	0	Scanner keyboard = new Scanner(System.in);
29	0	String command = keyboard.nextLine();
30
31	0	Scanner inputScanner = new Scanner(command);
32		// prints family to console. Syntax is printFam <index>
33	0	if (command.indexOf("printFam") > -1)
34		{
35	0	try
36		{
37	0	inputScanner.next();
38	0	int index = inputScanner.nextInt();
39	0	analyser.printFam(index);
40	0	continue;
41		} catch (Exception e)
42		{
43	0	System.out.println("Command failed");
44		}
45
46		}
47		// prints HMM to console. Syntax is printHMM <index>
48	0	if (command.indexOf("printHMM") > -1)
49		{
50	0	try
51		{
52	0	inputScanner.next();
53	0	int index = inputScanner.nextInt();
54	0	analyser.printHMM(index);
55	0	continue;
56		} catch (Exception e)
57		{
58	0	System.out.println("Command failed");
59		}
60		}
61		// prints family to file in current folder. Syntax is exportFam <index>.
62	0	if (command.indexOf("exportFam") > -1)
63		{
64	0	try
65		{
66	0	inputScanner.next();
67	0	int index = inputScanner.nextInt();
68	0	String location = inputScanner.next();
69	0	analyser.exportFam(index, location);
70	0	continue;
71		} catch (Exception e)
72		{
73	0	System.out.println("Command failed");
74		}
75		}
76		// prints HMM to file in current folder. Syntax is exportHMM <index>.
77	0	if (command.indexOf("exportHMM") > -1)
78		{
79	0	try
80		{
81	0	inputScanner.next();
82	0	int index = inputScanner.nextInt();
83	0	String location = inputScanner.next();
84	0	analyser.exportHMM(index, location);
85	0	continue;
86		} catch (Exception e)
87		{
88	0	System.out.println("Command failed");
89		}
90		}
91		// Processes data. Syntax is run <number of loops> <increments>. The
92		// number loops specifies the number of increments the program will run.
93		// After each increment, the data stored currently in the program is
94		// exported and re-read back into the program. This is to ensure that the
95		// program can be terminated without losing a large quantity of data. The
96		// increment is the number of families read per 'save'.
97	0	if (command.indexOf("run") > -1 && !(command.indexOf("ToEnd") > -1))
98		{
99	0	try
100		{
101
102	0	inputScanner.next();
103
104	0	int loops = inputScanner.nextInt();
105	0	int increments = inputScanner.nextInt();
106	0	boolean keepRaw = inputScanner.nextBoolean();
107
108	0	for (int i = 0; i < loops; i++)
109		{
110	0	analyser.run(increments, keepRaw);
111	0	System.out.println("Saved");
112		}
113	0	System.out.println("Task completed");
114	0	continue;
115		} catch (Exception e)
116		{
117	0	System.out.println("Command failed");
118		}
119	0	continue;
120		}
121	0	if ((command.indexOf("runToEnd") > -1))
122		{
123	0	try
124		{
125
126	0	inputScanner.next();
127	0	int minCount = inputScanner.nextInt();
128	0	int maxCount = inputScanner.nextInt();
129	0	boolean keepRaw = inputScanner.nextBoolean();
130	0	boolean forClans = inputScanner.nextBoolean();
131	0	analyser.runToEnd(minCount, maxCount, keepRaw, forClans);
132	0	System.out.println("Task completed");
133		} catch (Exception e)
134		{
135	0	System.out.println("Command failed");
136		}
137	0	continue;
138		}
139		// terminates program. Syntax is terminate.
140	0	if (command.indexOf("terminate") > -1)
141		{
142	0	running = false;
143	0	continue;
144		}
145		// clears files in current directory (Only a specific set of files).
146		// Syntax is clear.
147	0	if (command.indexOf("clear") > -1)
148		{
149	0	analyser.clear();
150	0	continue;
151		}
152		// changes current directory. Syntax is cd <directory>
153	0	if (command.indexOf("cd") > -1)
154		{
155	0	try
156		{
157	0	inputScanner.next();
158	0	analyser.setFolder(inputScanner.next());
159		} catch (Exception e)
160		{
161	0	System.out.println("Command failed");
162
163		}
164	0	continue;
165		}
166
167	0	if (command.indexOf("getFamName") > -1)
168		{
169	0	try
170		{
171	0	inputScanner.next();
172	0	System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
173
174		} catch (Exception e)
175		{
176	0	System.out.println("Command failed");
177		}
178	0	continue;
179		}
180	0	if (command.indexOf("sortIntoClans") > -1)
181		{
182	0	inputScanner.next();
183	0	analyser.sortIntoClans(inputScanner.next());
184	0	continue;
185
186		}
187	0	if (command.indexOf("setFamilies") > -1)
188		{
189	0	inputScanner.next();
190	0	analyser.setFamilies(inputScanner.next());
191	0	continue;
192
193		}
194
195	0	if (command.indexOf("setHMMs") > -1)
196		{
197	0	inputScanner.next();
198	0	analyser.setHmms(inputScanner.next());
199	0	continue;
200
201		}
202
203	0	if (command.indexOf("alignWithinClans") > -1)
204		{
205	0	inputScanner.next();
206	0	String export = inputScanner.next();
207	0	String clans = inputScanner.next();
208	0	analyser.alignWithinClan(export, clans);
209	0	continue;
210
211		}
212
213	0	System.out.println("Unrecognised command");
214		}
215
216
217
218
219		}
220
221		}